DEMO_febio_0035_blob_shear_contact_hex8

Below is a demonstration for:

Contents

Keywords

clear; close all; clc;

Plot settings

fontSize=15;
faceAlpha1=0.8;
faceAlpha2=0.3;
markerSize=40;
markerSize2=15;
lineWidth=3;

Control parameters

% Path names
defaultFolder = fileparts(fileparts(mfilename('fullpath')));
savePath=fullfile(defaultFolder,'data','temp');

% Defining file names
febioFebFileNamePart='tempModel';
febioFebFileName=fullfile(savePath,[febioFebFileNamePart,'.feb']); %FEB file name
febioLogFileName=fullfile(savePath,[febioFebFileNamePart,'.txt']); %FEBio log file name
febioLogFileName_disp=[febioFebFileNamePart,'_disp_out.txt']; %Log file name for exporting displacement

% Hemi-sphere parameters
hemiSphereRadius=6;
numElementsMantel=4;
smoothEdge=1;
solidElementType='hex8';%'hex20';
membraneThickness=0.1;

% Ground plate parameters
plateRadius=1.3*hemiSphereRadius;

% Probe parameters
probeWidth=3*hemiSphereRadius;
filletProbe=hemiSphereRadius/2; %Fillet radius

% Define probe displacement
probeDisplacement=hemiSphereRadius*2;
probeOverlapFactor=0.3;
probeLength=hemiSphereRadius*2;

% Material parameter set
l=1e-3;
lt=1000*l;
m=1e-3;
mt=1000*m;

mu1=mt;
mu2=mt;
mu3=m;
lambda11=lt;
lambda22=lt;
lambda12=lt;
lambda33=l;
lambda23=l;
lambda13=l;
[E1,E2,E3,G12,G23,G31,v12,v23,v31]=lameInvertHookeOrthotropic(mu1,mu2,mu3,lambda11,lambda22,lambda33,lambda12,lambda23,lambda13);

materialPropertiesFung.E1=E1;
materialPropertiesFung.E2=E2;
materialPropertiesFung.E3=E3;
materialPropertiesFung.G12=G12;
materialPropertiesFung.G23=G23;
materialPropertiesFung.G31=G31;
materialPropertiesFung.v12=v12;
materialPropertiesFung.v23=v23;
materialPropertiesFung.v31=v31;
materialPropertiesFung.c=10;
materialPropertiesFung.k=1000*mean([G12 G23 G31]);

%Ogden parameters
materialPropertiesOgden.c1=1e-3; %Shear-modulus-like parameter
materialPropertiesOgden.m1=2; %Material parameter setting degree of non-linearity
materialPropertiesOgden.k=1000*materialPropertiesOgden.c1; %Bulk modulus

% FEA control settings
numTimeSteps=25;
max_refs=25; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=15; %Optimum number of iterations
max_retries=25; %Maximum number of retires
symmetric_stiffness=0;
min_residual=1e-20;
step_size=1/numTimeSteps;
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=(1/numTimeSteps); %Maximum time step size

%Contact parameters
contactPenalty=0.01;
laugon=0;
minaug=1;
maxaug=10;
fric_coeff=0;
max_traction=0;

Creating model geometry and mesh

%Control settings
optionStruct.sphereRadius=hemiSphereRadius;
optionStruct.coreRadius=optionStruct.sphereRadius/2;
optionStruct.numElementsMantel=numElementsMantel;
optionStruct.numElementsCore=optionStruct.numElementsMantel*2;
optionStruct.outputStructType=2;
optionStruct.makeHollow=0;
optionStruct.cParSmooth.n=25;

% %Creating sphere
[meshStruct]=hexMeshHemiSphere(optionStruct);

% Access model element and patch data
Fb_blob=meshStruct.facesBoundary;
Cb_blob=meshStruct.boundaryMarker;
V_blob=meshStruct.nodes;
E_blob=meshStruct.elements;

F_blob=element2patch(E_blob);

pointSpacingBlob=max(patchEdgeLengths(Fb_blob,V_blob));

%Smoothen edges
if smoothEdge==1
    %Get rigid region
    ind=1:1:size(V_blob,1); %Indices for all nodes
    indRigid1=find(ismember(ind,Fb_blob(Cb_blob==2,:)) & ~ismember(ind,Fb_blob(Cb_blob==1,:))); %Indices for new bottom surface nodes
    indRigid2=find(ismember(ind,Fb_blob(Cb_blob==1,:)) & ~ismember(ind,Fb_blob(Cb_blob==2,:))); %Indices for new bottom surface nodes
    indRigid=[indRigid1(:); indRigid2(:);];

    %Smoothing
    cPar.Method='HC';
    cPar.n=250;
    cPar.RigidConstraints=indRigid;
    [Vb_blob]=patchSmooth(F_blob,V_blob,[],cPar);
    indSmooth=unique(F_blob(:));
    V_blob(indSmooth,:)=Vb_blob(indSmooth,:);
    %Fix color data with new bottom surface
    Cb_blob=ones(size(Cb_blob));
    Cb_blob(all(ismember(Fb_blob,indRigid1),2))=2;

    meshStruct.nodes=V_blob;
end

if strcmp(solidElementType,'hex20')
    [E_blob,V_blob,~,~,Fb_blob]=hex8_hex20(E_blob,V_blob,{},Fb_blob);
    [Fb_blob_plot]=element2patch(Fb_blob,[],'quad8');

    meshStruct.elements=E_blob;
    meshStruct.nodes=V_blob;
    meshStruct.Fb=Fb_blob_plot;
    shellElementType='quad8';
else
    Fb_blob_plot=Fb_blob;
    shellElementType='quad4';
end

Visualize blob mesh

hFig=cFigure;
subplot(1,2,1); hold on;
hp=gpatch(Fb_blob_plot,V_blob,Cb_blob,'k',1);
hp.Marker='.';
hp.MarkerSize=markerSize2;

% patchNormPlot(Fb_blob,V_blob);
% plotV(V_blob(indRigid,:),'g.','MarkerSize',25);
axisGeom(gca,fontSize);
colormap(gjet); icolorbar;
camlight headlight;

hs=subplot(1,2,2); hold on;
title('Cut view of solid mesh','FontSize',fontSize);
optionStruct.hFig=[hFig hs];
gpatch(Fb_blob_plot,V_blob,'kw','none',0.25);
meshView(meshStruct,optionStruct);
axisGeom(gca,fontSize);
drawnow;

Creating rigid body shear surface

pointSpacingProbe=pointSpacingBlob/2;

%Sketching side profile
d=hemiSphereRadius*cos(asin(1-probeOverlapFactor));
x=[-probeLength-hemiSphereRadius -d -d];
y=[0 0 0];
z=[hemiSphereRadius*(1-probeOverlapFactor) hemiSphereRadius*(1-probeOverlapFactor) hemiSphereRadius*1.5];
V_probe_curve_sketch=[x(:) y(:) z(:)];

%Fillet sketch
np=100; %Number of points used to construct each fillet edge
[V_probe_curve]=filletCurve(V_probe_curve_sketch,filletProbe,np,0);
numPointsProbeCurve=ceil(max(pathLength(V_probe_curve))/pointSpacingProbe);
[V_probe_curve] = evenlySampleCurve(V_probe_curve,numPointsProbeCurve,'pchip',0);

% Extruding curve
% controlParametersExtrude.pointSpacing=pointSpacingProbe;
controlParametersExtrude.depth=hemiSphereRadius*2.5;
controlParametersExtrude.numSteps=ceil(controlParametersExtrude.depth/pointSpacingProbe);
controlParametersExtrude.numSteps=controlParametersExtrude.numSteps+iseven(controlParametersExtrude.numSteps); %Force uneven
controlParametersExtrude.patchType='quad';
controlParametersExtrude.dir=0;
controlParametersExtrude.n=[0 1 0];
controlParametersExtrude.closeLoopOpt=0;

[F_probe,V_probe]=polyExtrude(V_probe_curve,controlParametersExtrude);
F_probe=fliplr(F_probe); %Invert face orientation so normals point to blob

if strcmp(solidElementType,'hex20')
    [F_probe,V_probe]=quad4_quad8(F_probe,V_probe);
    [F_probe_plot]=element2patch(F_probe,[],'quad8');
else
    F_probe_plot=F_probe;
end

center_of_mass_probe=mean(V_probe,1);

Visualizing probe mesh

cFigure; hold on;
title('The probe surface mesh','fontSize',fontSize);
gpatch(Fb_blob_plot,V_blob,'kw','none',0.5);
hl(1)=plotV(V_probe_curve_sketch,'k.-.','lineWidth',3,'MarkerSize',25);
hl(2)=plotV(V_probe_curve,'r-','lineWidth',3,'MarkerSize',25);
hl(3)=gpatch(F_probe_plot,V_probe,'gw','k',1);
% hl(3).Marker='.';
% hl(3).MarkerSize=markerSize2;
legend(hl,{'Sketched probe curve','Rounded probe curve','Probe surface mesh'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Join model node sets

V=[V_blob; V_probe];
F_probe=F_probe+size(V_blob,1);
F_probe_plot=F_probe_plot+size(V_blob,1);

Visualizing model

cFigure; hold on;
gtitle('Model components',fontSize);
hl(1)=gpatch(Fb_blob_plot,V,'rw','k',0.8);
hl(2)=gpatch(F_probe_plot,V,'gw','k',0.8);
legend(hl,{'Blob','Probe'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Get local material axes

[N3,Vn]=patchNormal(Fb_blob_plot,V);
[N1,N2]=vectorOrthogonalPair(N3); %Get orthogonal vector pair

Visualizing axes

cFigure; hold on;
gtitle('Local material axes',fontSize);
hl(1)=gpatch(Fb_blob_plot,V,'w','k',1);
hl(2)=quiverVec(Vn,N1,pointSpacingBlob,'y');
hl(3)=quiverVec(Vn,N2,pointSpacingBlob,'g');
hl(4)=quiverVec(Vn,N3,pointSpacingBlob,'b');
legend(hl,{'Blob','1st axis','2nd axis','3rd axis'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;
drawnow;

Get contact surfaces

Visualize contact surfaces

cFigure;
title('Probe blob contact pair','fontsize',fontSize);
hl(1)=gpatch(F_probe_plot,V,'rw','k',1);
patchNormPlot(F_probe_plot,V);
hl(2)=gpatch(Fb_blob_plot,V,'gw','k',1);
patchNormPlot(Fb_blob_plot,V);
legend(hl,{'Master','Slave'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;

drawnow;

Setup boundary conditions

bcSupportList=unique(Fb_blob(Cb_blob==2,:));

Visualize boundary condition sets

cFigure; hold on;
title('Boundary conditions ','fontsize',fontSize);
gpatch(F_probe_plot,V,'kw','none',0.2);
gpatch(Fb_blob_plot,V,'kw','none',0.2);
hl(1)=plotV(V(bcSupportList,:),'k.','MarkerSize',markerSize);

legend(hl,{'Supported nodes'}); clear hl;
axisGeom(gca,fontSize);
camlight headlight;

drawnow;

Defining the FEBio input structure

See also febioStructTemplate and febioStruct2xml and the FEBio user manual.

%Get a template with default settings
[febio_spec]=febioStructTemplate;

%febio_spec version
febio_spec.ATTR.version='3.0';

%Module section
febio_spec.Module.ATTR.type='solid';

%Control section
febio_spec.Control.analysis='STATIC';
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=1/numTimeSteps;
febio_spec.Control.solver.max_refs=max_refs;
febio_spec.Control.solver.max_ups=max_ups;
febio_spec.Control.solver.symmetric_stiffness=0;
febio_spec.Control.time_stepper.dtmin=dtmin;
febio_spec.Control.time_stepper.dtmax=dtmax;
febio_spec.Control.time_stepper.max_retries=max_retries;
febio_spec.Control.time_stepper.opt_iter=opt_iter;

%Material section
materialName1='Material1';
febio_spec.Material.material{1}.ATTR.name=materialName1;
febio_spec.Material.material{1}.ATTR.type='Ogden';
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.c1=materialPropertiesOgden.c1;
febio_spec.Material.material{1}.m1=materialPropertiesOgden.m1;
febio_spec.Material.material{1}.c2=materialPropertiesOgden.c1;
febio_spec.Material.material{1}.m2=-materialPropertiesOgden.m1;
febio_spec.Material.material{1}.k=materialPropertiesOgden.k;

materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
febio_spec.Material.material{2}.ATTR.type='Fung orthotropic';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.E1=materialPropertiesFung.E1;
febio_spec.Material.material{2}.E2=materialPropertiesFung.E2;
febio_spec.Material.material{2}.E3=materialPropertiesFung.E3;
febio_spec.Material.material{2}.G12=materialPropertiesFung.G12;
febio_spec.Material.material{2}.G23=materialPropertiesFung.G23;
febio_spec.Material.material{2}.G31=materialPropertiesFung.G31;
febio_spec.Material.material{2}.v12=materialPropertiesFung.v12;
febio_spec.Material.material{2}.v23=materialPropertiesFung.v23;
febio_spec.Material.material{2}.v31=materialPropertiesFung.v31;
febio_spec.Material.material{2}.c=materialPropertiesFung.c;
febio_spec.Material.material{2}.k=materialPropertiesFung.k;

materialName3='Material3';
febio_spec.Material.material{3}.ATTR.name=materialName3;
febio_spec.Material.material{3}.ATTR.type='rigid body';
febio_spec.Material.material{3}.ATTR.id=3;
febio_spec.Material.material{3}.density=1;
febio_spec.Material.material{3}.center_of_mass=center_of_mass_probe;

%Mesh section
% -> Nodes
febio_spec.Mesh.Nodes{1}.ATTR.name='nodeSet_all'; %The node set name
febio_spec.Mesh.Nodes{1}.node.ATTR.id=(1:size(V,1))'; %The node id's
febio_spec.Mesh.Nodes{1}.node.VAL=V; %The nodel coordinates

% -> Elements
partName1='Part1';
febio_spec.Mesh.Elements{1}.ATTR.name=partName1; %Name of this part
febio_spec.Mesh.Elements{1}.ATTR.type=solidElementType; %Element type
febio_spec.Mesh.Elements{1}.elem.ATTR.id=(1:1:size(E_blob,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E_blob; %The element matrix

partName2='Part2';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part
febio_spec.Mesh.Elements{2}.ATTR.type=shellElementType; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E_blob,1)+(1:1:size(Fb_blob,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=Fb_blob;

partName3='Part3';
febio_spec.Mesh.Elements{3}.ATTR.name=partName3; %Name of this part
febio_spec.Mesh.Elements{3}.ATTR.type=shellElementType; %Element type
febio_spec.Mesh.Elements{3}.elem.ATTR.id=size(E_blob,1)+size(Fb_blob,1)+(1:1:size(F_probe,1))'; %Element id's
febio_spec.Mesh.Elements{3}.elem.VAL=F_probe;

% -> NodeSets
nodeSetName1='bcSupportList';
febio_spec.Mesh.NodeSet{1}.ATTR.name=nodeSetName1;
febio_spec.Mesh.NodeSet{1}.node.ATTR.id=bcSupportList(:);

%MeshDomains section
febio_spec.MeshDomains.SolidDomain.ATTR.name=partName1;
febio_spec.MeshDomains.SolidDomain.ATTR.mat=materialName1;

febio_spec.MeshDomains.ShellDomain{1}.ATTR.name=partName2;
febio_spec.MeshDomains.ShellDomain{1}.ATTR.mat=materialName2;

febio_spec.MeshDomains.ShellDomain{2}.ATTR.name=partName3;
febio_spec.MeshDomains.ShellDomain{2}.ATTR.mat=materialName3;

% % -> Surfaces
surfaceName1='contactSurface1';
febio_spec.Mesh.Surface{1}.ATTR.name=surfaceName1;
febio_spec.Mesh.Surface{1}.(shellElementType).ATTR.id=(1:1:size(F_probe,1))';
febio_spec.Mesh.Surface{1}.(shellElementType).VAL=F_probe;

surfaceName2='contactSurface2';
febio_spec.Mesh.Surface{2}.ATTR.name=surfaceName2;
febio_spec.Mesh.Surface{2}.(shellElementType).ATTR.id=(1:1:size(Fb_blob(Cb_blob==1,:),1))';
febio_spec.Mesh.Surface{2}.(shellElementType).VAL=Fb_blob(Cb_blob==1,:);

% -> Surface pairs
contactPairName1='Contact1';
febio_spec.Mesh.SurfacePair{1}.ATTR.name=contactPairName1;
febio_spec.Mesh.SurfacePair{1}.primary=surfaceName1;
febio_spec.Mesh.SurfacePair{1}.secondary=surfaceName2;

%MeshData section
% -> ElementData
febio_spec.MeshData.ElementData{1}.ATTR.var='shell thickness';
febio_spec.MeshData.ElementData{1}.ATTR.elem_set=partName2;
febio_spec.MeshData.ElementData{1}.elem.ATTR.lid=(1:1:size(Fb_blob,1))';
febio_spec.MeshData.ElementData{1}.elem.VAL=membraneThickness.*ones(size(Fb_blob));

%MeshData section
% -> ElementData
febio_spec.MeshData.ElementData{2}.ATTR.elem_set=partName2;
febio_spec.MeshData.ElementData{2}.ATTR.var='mat_axis';

for q=1:1:size(N1,1)
    febio_spec.MeshData.ElementData{2}.elem{q}.ATTR.lid=q;
    febio_spec.MeshData.ElementData{2}.elem{q}.a=N1(q,:);
    febio_spec.MeshData.ElementData{2}.elem{q}.d=N2(q,:);
end

%Boundary condition section
% -> Fix boundary conditions
febio_spec.Boundary.bc{1}.ATTR.type='fix';
febio_spec.Boundary.bc{1}.ATTR.node_set=nodeSetName1;
febio_spec.Boundary.bc{1}.dofs='x,y,z';

%Rigid section
% -> Prescribed rigid body boundary conditions
febio_spec.Rigid.rigid_constraint{1}.ATTR.name='RigidFix_1';
febio_spec.Rigid.rigid_constraint{1}.ATTR.type='fix';
febio_spec.Rigid.rigid_constraint{1}.rb=3;
febio_spec.Rigid.rigid_constraint{1}.dofs='Ry,Rz,Ru,Rv,Rw';

febio_spec.Rigid.rigid_constraint{2}.ATTR.name='RigidPrescribe';
febio_spec.Rigid.rigid_constraint{2}.ATTR.type='prescribe';
febio_spec.Rigid.rigid_constraint{2}.rb=3;
febio_spec.Rigid.rigid_constraint{2}.dof='Rx';
febio_spec.Rigid.rigid_constraint{2}.value.ATTR.lc=1;
febio_spec.Rigid.rigid_constraint{2}.value.VAL=probeDisplacement;
febio_spec.Rigid.rigid_constraint{2}.relative=0;

%Contact section
febio_spec.Contact.contact{1}.ATTR.surface_pair=contactPairName1;
febio_spec.Contact.contact{1}.ATTR.type='sliding-elastic';
febio_spec.Contact.contact{1}.two_pass=1;
febio_spec.Contact.contact{1}.laugon=laugon;
febio_spec.Contact.contact{1}.tolerance=0.2;
febio_spec.Contact.contact{1}.gaptol=0;
febio_spec.Contact.contact{1}.minaug=minaug;
febio_spec.Contact.contact{1}.maxaug=maxaug;
febio_spec.Contact.contact{1}.search_tol=0.01;
febio_spec.Contact.contact{1}.search_radius=0.1;
febio_spec.Contact.contact{1}.symmetric_stiffness=0;
febio_spec.Contact.contact{1}.auto_penalty=1;
febio_spec.Contact.contact{1}.penalty=contactPenalty;
febio_spec.Contact.contact{1}.fric_coeff=fric_coeff;

%LoadData section
% -> load_controller
febio_spec.LoadData.load_controller{1}.ATTR.id=1;
febio_spec.LoadData.load_controller{1}.ATTR.type='loadcurve';
febio_spec.LoadData.load_controller{1}.interpolate='LINEAR';
febio_spec.LoadData.load_controller{1}.points.point.VAL=[0 0; 1 1];

%Output section
% -> log file
febio_spec.Output.logfile.ATTR.file=febioLogFileName;
febio_spec.Output.logfile.node_data{1}.ATTR.file=febioLogFileName_disp;
febio_spec.Output.logfile.node_data{1}.ATTR.data='ux;uy;uz';
febio_spec.Output.logfile.node_data{1}.ATTR.delim=',';

Quick viewing of the FEBio input file structure

The febView function can be used to view the xml structure in a MATLAB figure window.

febView(febio_spec); %Viewing the febio file

Exporting the FEBio input file

Exporting the febio_spec structure to an FEBio input file is done using the febioStruct2xml function.

febioStruct2xml(febio_spec,febioFebFileName); %Exporting to file and domNode

Running the FEBio analysis

To run the analysis defined by the created FEBio input file the runMonitorFEBio function is used. The input for this function is a structure defining job settings e.g. the FEBio input file name. The optional output runFlag informs the user if the analysis was run succesfully.

febioAnalysis.run_filename=febioFebFileName; %The input file name
febioAnalysis.run_logname=febioLogFileName; %The name for the log file
febioAnalysis.disp_on=1; %Display information on the command window
febioAnalysis.runMode='external';%'internal';

[runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 16-Dec-2020 11:57:07
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files                16-Dec-2020 11:57:07
 * Removal succesful                                   16-Dec-2020 11:57:07
# Attempt removal of existing .xplt files              16-Dec-2020 11:57:07
 * Removal succesful                                   16-Dec-2020 11:57:07
# Starting FEBio...                                    16-Dec-2020 11:57:07
  Max. total analysis time is: Inf s
 * Waiting for log file creation                       16-Dec-2020 11:57:07
   Max. wait time: 30 s
 * Log file found.                                     16-Dec-2020 11:57:07
# Parsing log file...                                  16-Dec-2020 11:57:07
    number of iterations   : 1                         16-Dec-2020 11:57:07
    number of reformations : 1                         16-Dec-2020 11:57:07
------- converged at time : 0.04                       16-Dec-2020 11:57:07
    number of iterations   : 1                         16-Dec-2020 11:57:07
    number of reformations : 1                         16-Dec-2020 11:57:07
------- converged at time : 0.08                       16-Dec-2020 11:57:07
    number of iterations   : 1                         16-Dec-2020 11:57:08
    number of reformations : 1                         16-Dec-2020 11:57:08
------- converged at time : 0.12                       16-Dec-2020 11:57:08
    number of iterations   : 1                         16-Dec-2020 11:57:08
    number of reformations : 1                         16-Dec-2020 11:57:08
------- converged at time : 0.16                       16-Dec-2020 11:57:08
    number of iterations   : 8                         16-Dec-2020 11:57:09
    number of reformations : 8                         16-Dec-2020 11:57:09
------- converged at time : 0.2                        16-Dec-2020 11:57:09
    number of iterations   : 13                        16-Dec-2020 11:57:11
    number of reformations : 13                        16-Dec-2020 11:57:11
------- converged at time : 0.238462                   16-Dec-2020 11:57:11
    number of iterations   : 13                        16-Dec-2020 11:57:13
    number of reformations : 13                        16-Dec-2020 11:57:13
------- converged at time : 0.275554                   16-Dec-2020 11:57:13
    number of iterations   : 10                        16-Dec-2020 11:57:15
    number of reformations : 10                        16-Dec-2020 11:57:15
------- converged at time : 0.311426                   16-Dec-2020 11:57:15
    number of iterations   : 12                        16-Dec-2020 11:57:16
    number of reformations : 12                        16-Dec-2020 11:57:16
------- converged at time : 0.348124                   16-Dec-2020 11:57:16
    number of iterations   : 10                        16-Dec-2020 11:57:17
    number of reformations : 10                        16-Dec-2020 11:57:17
------- converged at time : 0.385212                   16-Dec-2020 11:57:17
    number of iterations   : 10                        16-Dec-2020 11:57:18
    number of reformations : 10                        16-Dec-2020 11:57:18
------- converged at time : 0.422883                   16-Dec-2020 11:57:18
    number of iterations   : 12                        16-Dec-2020 11:57:20
    number of reformations : 12                        16-Dec-2020 11:57:20
------- converged at time : 0.461019                   16-Dec-2020 11:57:20
    number of iterations   : 12                        16-Dec-2020 11:57:21
    number of reformations : 12                        16-Dec-2020 11:57:21
------- converged at time : 0.499375                   16-Dec-2020 11:57:21
    number of iterations   : 11                        16-Dec-2020 11:57:23
    number of reformations : 11                        16-Dec-2020 11:57:23
------- converged at time : 0.536443                   16-Dec-2020 11:57:23
    number of iterations   : 12                        16-Dec-2020 11:57:27
    number of reformations : 12                        16-Dec-2020 11:57:27
------- converged at time : 0.568224                   16-Dec-2020 11:57:27
    number of iterations   : 10                        16-Dec-2020 11:57:28
    number of reformations : 10                        16-Dec-2020 11:57:28
------- converged at time : 0.600975                   16-Dec-2020 11:57:28
    number of iterations   : 10                        16-Dec-2020 11:57:29
    number of reformations : 10                        16-Dec-2020 11:57:29
------- converged at time : 0.635176                   16-Dec-2020 11:57:29
    number of iterations   : 9                         16-Dec-2020 11:57:30
    number of reformations : 9                         16-Dec-2020 11:57:30
------- converged at time : 0.670537                   16-Dec-2020 11:57:30
    number of iterations   : 8                         16-Dec-2020 11:57:31
    number of reformations : 8                         16-Dec-2020 11:57:31
------- converged at time : 0.706826                   16-Dec-2020 11:57:31
    number of iterations   : 8                         16-Dec-2020 11:57:32
    number of reformations : 8                         16-Dec-2020 11:57:32
------- converged at time : 0.743856                   16-Dec-2020 11:57:32
    number of iterations   : 8                         16-Dec-2020 11:57:32
    number of reformations : 8                         16-Dec-2020 11:57:32
------- converged at time : 0.781481                   16-Dec-2020 11:57:32
    number of iterations   : 7                         16-Dec-2020 11:57:33
    number of reformations : 7                         16-Dec-2020 11:57:33
------- converged at time : 0.819581                   16-Dec-2020 11:57:33
    number of iterations   : 7                         16-Dec-2020 11:57:34
    number of reformations : 7                         16-Dec-2020 11:57:34
------- converged at time : 0.858061                   16-Dec-2020 11:57:34
    number of iterations   : 7                         16-Dec-2020 11:57:35
    number of reformations : 7                         16-Dec-2020 11:57:35
------- converged at time : 0.896845                   16-Dec-2020 11:57:35
    number of iterations   : 7                         16-Dec-2020 11:57:36
    number of reformations : 7                         16-Dec-2020 11:57:36
------- converged at time : 0.935872                   16-Dec-2020 11:57:36
    number of iterations   : 8                         16-Dec-2020 11:57:37
    number of reformations : 8                         16-Dec-2020 11:57:37
------- converged at time : 0.975093                   16-Dec-2020 11:57:37
    number of iterations   : 8                         16-Dec-2020 11:57:38
    number of reformations : 8                         16-Dec-2020 11:57:38
------- converged at time : 1                          16-Dec-2020 11:57:38
 Elapsed time : 0:00:31                                16-Dec-2020 11:57:38
 N O R M A L   T E R M I N A T I O N
# Done                                                 16-Dec-2020 11:57:38
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Import FEBio results

if 1%runFlag==1 %i.e. a succesful run

Importing nodal displacements from a log file

    dataStruct=importFEBio_logfile(fullfile(savePath,febioLogFileName_disp),1,1);

    %Access data
    N_disp_mat=dataStruct.data; %Displacement
    timeVec=dataStruct.time; %Time

    %Create deformed coordinate set
    V_DEF=N_disp_mat+repmat(V,[1 1 size(N_disp_mat,3)]);

Plotting the simulated results using anim8 to visualize and animate deformations

    DN_magnitude=sqrt(sum(N_disp_mat(:,:,end).^2,2)); %Current displacement magnitude

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; hold on;
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp1=gpatch(Fb_blob_plot,V_DEF(:,:,end),DN_magnitude,'k',1); %Add graphics object to animate
    hp1.FaceColor='interp';
    hp2=gpatch(F_probe_plot,V_DEF(:,:,end),'kw','none',0.5); %Add graphics object to animate
%     gpatch(Fb_all,V,0.5*ones(1,3),'none',0.25); %A static graphics object

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(DN_magnitude(Fb_blob_plot(:)))]); caxis manual;
    axis(axisLim(V_DEF)); %Set axis limits statically
    camlight headlight;
    view(15,8);
    drawnow;
    % Set up animation features
    animStruct.Time=timeVec; %The time vector
    for qt=1:1:size(N_disp_mat,3) %Loop over time increments
        DN_magnitude=sqrt(sum(N_disp_mat(:,:,qt).^2,2)); %Current displacement magnitude

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp1 hp1 hp2]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices'}; %Properties of objects to animate
        animStruct.Set{qt}={V_DEF(:,:,qt),DN_magnitude,V_DEF(:,:,qt)}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    drawnow;

end

GIBBON www.gibboncode.org

Kevin Mattheus Moerman, [email protected]

GIBBON footer text

License: https://github.com/gibbonCode/GIBBON/blob/master/LICENSE

GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for image segmentation, image-based modeling, meshing, and finite element analysis.

Copyright (C) 2006-2020 Kevin Mattheus Moerman

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Published with MATLAB® R2020b